An accountancy body says it is "simply unfair" that people owing tax have seen a rise in the interest they pay, while those owed a refund will see no change.
The interest charged to anyone paying their tax late has increased in line with the rise in the Bank rate.
But the HM Revenue and Customs (HMRC) repayment rate has been frozen.
The ACCA accountancy body said there should be a level playing field, but HMRC said the repayment rate never went below 0.5%.
The interest rate charged to people who pay their tax late has risen by 0.25 percentage points to 3.25%.
However, the amount paid by HMRC on top of the amount it refunds to those who have overpaid tax is 0.5%, and has been since 2009.
The theory is that HMRC does not want people to use overpayments to secure a better interest rate than they might get on a savings account.
The tax authority said that the formula for the repayment rate had not changed. This meant it would remain at 0.5% until the Bank rate rose higher than 1.5%.
"The rate we pay on repayments never falls below 0.5%, even when the Bank of England base rate is low," a spokesman for HMRC said.
"The different interest rates provide fairness to taxpayers who pay on time. Most people pay their tax on time and it is only right that those who don't, pay a higher rate of interest on the unpaid tax that would otherwise have gone to our schools, hospitals and other vital public services."
However, Chas Roy-Chowdhury, head of taxation at ACCA, said that there should be a level playing field, so HMRC should have made the same change to the rate it charges and the rate it pays.
About 10 million people are in the self-assessment system for income tax. The deadline for online filing is 31 January. Those submitting forms on paper needed to do so by 31 October.